Open Access Highly Accessed Research article

Transcriptome analysis of bitter acid biosynthesis and precursor pathways in hop (Humulus lupulus)

Shawn M Clark1, Vinidhra Vaitheeswaran1, Stephen J Ambrose1, Randy W Purves1 and Jonathan E Page12*

Author Affiliations

1 National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada

2 Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK, S7N 5E2, Canada

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BMC Plant Biology 2013, 13:12  doi:10.1186/1471-2229-13-12

Published: 24 January 2013

Additional files

Additional file 1 Table S1:

Total Illumina sequencing reads for each RNA sample and the number of reads that mapped to the reference transcriptome.

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Additional file 2 Table S2:

RNA-seq analysis of metabolic genes compared between lupulin gland and leaf, lupulin gland and cone (minus glands), and leaf and cone (minus glands). Data is represented in reads per kb exon model per million mapped reads (RPKM). Note that each tissue comparison is located on a separate Excel sheet.

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Additional file 3 Table S3:

Transcript abundance of transcription factors compared between lupulin gland and leaf, lupulin gland and cone (minus glands) and leaf and cone (minus glands). Data is represented in RPKM.

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Additional file 4 Figure S1:

Relative abundance of select metabolic transcripts in lupulin gland and leaf samples as determined by qRT-PCR. Data is presented using relative quantitation (RQ) based on ΔΔCT values. Samples are normalized using β-tubulin. Data represents the mean and standard error, n=3. Transcript abundance between panels a, b and c is not directly comparable in this figure. a) qRT-PCR analysis of HlBCAT1 and HlBCAT2. A single gland sample was used as reference. b) qRT-PCR analysis of genes encoding enzymes of the BCKDH complex (ketoacid dehydrogenase E1α and E1β, dihydrolipoyl acyltransferase (E2), and dihydrolipoyl dehydrogenase (E3)). A single leaf sample was used as reference. c) qRT-PCR analysis of VPS and HlPT1. A single leaf sample was used as reference.

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Additional file 5 Figure S2:

Subcellular co-localization of GFP fusion proteins of HlBCAT1 and HlBCAT2, with and without N-terminal signal peptides, compared with organelle specific marker proteins using transient expression in Nicotiana benthamiana leaves. MTRK and PTRK are mitochondrial and plastidial makers. Scale bars represent 20 μm.

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Additional file 6 Table S4:

RPKM values for lupulin glands, cones (minus glands) and leaves.

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Additional file 7 Table S5:

Sequences of oligonucleotides used.

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